--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_rfam_express.pl	Thu Sep 18 21:40:25 2014 -0400
@@ -0,0 +1,1800 @@
+#!/usr/bin/perl -w
+#Filename:
+#Author: Tian Dongmei
+#Email: tiandm@big.ac.cn
+#Date: 2013/7/19
+#Modified:
+#Description: 
+my $version=1.00;
+
+use strict;
+use Getopt::Long;
+use File::Basename;
+
+my %opts;
+GetOptions(\%opts,"i=s","o=s","tag:s","h");
+if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
+&usage;
+}
+
+my $filein=$opts{'i'};
+my $fileout=$opts{'o'};
+
+my $marks=defined $opts{'tag'} ? $opts{'tag'} : "";
+
+if(!(defined $opts{'tag'})){
+	my $line=`head -1 $filein`;
+	my @tmp=split/\t/,$line;
+	$tmp[0]=~/:([\d|_]+)_x(\d+)$/;
+	my @ss=split/_/,$1;
+	for (my $i=1;$i<=@ss;$i++) {
+		$marks .="Smp$i;";
+	}
+}
+
+my @marks=split/\;/,$marks;
+
+my %rfam_key;
+while(<DATA>){
+    chomp;
+    if(/^(\S+)\s+(\S+)$/){
+		$rfam_key{$1}=$2;
+    }
+}
+
+
+my %reads;
+my %tags;
+open IN,"<$filein";
+while (my $aline=<IN>) {
+	chomp $aline;
+	my @tmp=split/\t/,$aline;
+	$tmp[0]=~/:([\d|_]+)_x(\d+)$/;
+
+	my @exp=split/_/,$1;
+	my @tag=split/\;/,$tmp[2];
+
+	if (defined $rfam_key{$tag[0]}) {
+		for (my $i=0;$i<@exp;$i++) {
+			$reads{$rfam_key{$tag[0]}}[$i]+=$exp[$i];
+			$tags{$rfam_key{$tag[0]}}[$i]++ if($exp[$i]!=0);
+		}
+	}else{
+		for (my $i=0;$i<@exp;$i++) {
+			$reads{other}[$i]+=$exp[$i];
+			$tags{other}[$i]++ if($exp[$i]!=0);
+		}
+	}
+
+}
+close IN;
+
+$"="\t"; ##### @array print in \t
+open OUT,">$fileout";
+print OUT "####################################\n# small RNA expressed reads number #\n####################################\n";
+print OUT "#RNAname\t@marks\n";
+foreach my $key (keys %reads) {
+	print OUT $key;
+	for (my $i=0;$i<@{$reads{$key}} ;$i++) {
+		print OUT "\t",$reads{$key}[$i];
+	}
+	print OUT "\n";
+}
+
+print OUT "\n\n####################################\n# small RNA expressed tags number #\n####################################\n";
+print OUT "#RNAname\t@marks\n";
+
+foreach my $key (keys %tags) {
+	print OUT  $key;
+	for (my $i=0;$i<@{$reads{$key}} ;$i++) {
+		if(defined $tags{$key}[$i]){print OUT "\t",$tags{$key}[$i];}
+		else{print OUT "\t0";}
+	}
+	print OUT  "\n";
+}
+
+close OUT;
+$"=" "; ##### @array print in \t
+
+sub usage{
+print <<"USAGE";
+Version $version
+Usage:
+$0 -i -tag -o
+options:
+-i input file# rfam bowtie bwt. format mapping result
+-tag [string] sample marks# eg. sampleA;sampleB;sampleC
+-o output file
+
+-h help
+USAGE
+exit(1);
+}
+
+__DATA__
+RF00635	lncRNA
+RF01868	lncRNA
+RF01869	lncRNA
+RF01870	lncRNA
+RF01871	lncRNA
+RF01872	lncRNA
+RF01873	lncRNA
+RF01874	lncRNA
+RF01875	lncRNA
+RF01876	lncRNA
+RF01877	lncRNA
+RF01878	lncRNA
+RF01879	lncRNA
+RF01880	lncRNA
+RF01881	lncRNA
+RF01882	lncRNA
+RF01883	lncRNA
+RF01884	lncRNA
+RF01885	lncRNA
+RF01886	lncRNA
+RF01887	lncRNA
+RF01888	lncRNA
+RF01889	lncRNA
+RF01890	lncRNA
+RF01891	lncRNA
+RF01892	lncRNA
+RF01893	lncRNA
+RF01894	lncRNA
+RF01904	lncRNA
+RF01905	lncRNA
+RF01906	lncRNA
+RF01907	lncRNA
+RF01908	lncRNA
+RF01909	lncRNA
+RF01928	lncRNA
+RF01929	lncRNA
+RF01930	lncRNA
+RF01931	lncRNA
+RF01932	lncRNA
+RF01933	lncRNA
+RF01934	lncRNA
+RF01935	lncRNA
+RF01946	lncRNA
+RF01947	lncRNA
+RF01948	lncRNA
+RF01950	lncRNA
+RF01951	lncRNA
+RF01952	lncRNA
+RF01953	lncRNA
+RF01954	lncRNA
+RF01955	lncRNA
+RF01956	lncRNA
+RF01957	lncRNA
+RF01958	lncRNA
+RF01961	lncRNA
+RF01962	lncRNA
+RF01963	lncRNA
+RF01964	lncRNA
+RF01965	lncRNA
+RF01966	lncRNA
+RF01967	lncRNA
+RF01968	lncRNA
+RF01969	lncRNA
+RF01970	lncRNA
+RF01971	lncRNA
+RF01972	lncRNA
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+RF01974	lncRNA
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+RF01976	lncRNA
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+RF01978	lncRNA
+RF01979	lncRNA
+RF01980	lncRNA
+RF01981	lncRNA
+RF01983	lncRNA
+RF01984	lncRNA
+RF01985	lncRNA
+RF01986	lncRNA
+RF01987	lncRNA
+RF01992	lncRNA
+RF02038	lncRNA
+RF02039	lncRNA
+RF02040	lncRNA
+RF02041	lncRNA
+RF02042	lncRNA
+RF02043	lncRNA
+RF02044	lncRNA
+RF02045	lncRNA
+RF02046	lncRNA
+RF02047	lncRNA
+RF02085	lncRNA
+RF02086	lncRNA
+RF02087	lncRNA
+RF02089	lncRNA
+RF02090	lncRNA
+RF02091	lncRNA
+RF02098	lncRNA
+RF02101	lncRNA
+RF02102	lncRNA
+RF02103	lncRNA
+RF02104	lncRNA
+RF02105	lncRNA
+RF02106	lncRNA
+RF02107	lncRNA
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+RF02109	lncRNA
+RF02110	lncRNA
+RF02112	lncRNA
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+RF02114	lncRNA
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+RF02119	lncRNA
+RF02120	lncRNA
+RF02121	lncRNA
+RF02122	lncRNA
+RF02123	lncRNA
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+RF02125	lncRNA
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+RF02127	lncRNA
+RF02128	lncRNA
+RF02129	lncRNA
+RF02130	lncRNA
+RF02131	lncRNA
+RF02132	lncRNA
+RF02133	lncRNA
+RF02134	lncRNA
+RF02135	lncRNA
+RF02136	lncRNA
+RF02137	lncRNA
+RF02138	lncRNA
+RF02139	lncRNA
+RF02140	lncRNA
+RF02141	lncRNA
+RF02142	lncRNA
+RF02143	lncRNA
+RF02145	lncRNA
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+RF02148	lncRNA
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+RF02150	lncRNA
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+RF02168	lncRNA
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+RF02170	lncRNA
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+RF02174	lncRNA
+RF02175	lncRNA
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+RF02180	lncRNA
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+RF02190	lncRNA
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+RF02192	lncRNA
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+RF02195	lncRNA
+RF02196	lncRNA
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+RF02198	lncRNA
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+RF02200	lncRNA
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+RF02222	sRNA
+RF02223	sRNA
+RF02224	sRNA
+RF02225	sRNA
+RF02226	sRNA
+RF02227	sRNA
+RF02228	sRNA
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+RF02232	sRNA
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+RF02241	sRNA
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+RF02268	sRNA
+RF02269	sRNA
+RF00127	sRNA
+RF01852	tRNA
+RF00005	tRNA